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Title :   CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE

Authors :   L. R. Schofield, B. F. Anderson, M. L. Patchett, G. E. Norris, G. B. James E. J. Parker

Date :   12 Apr 05 (Deposition) - 18 Oct 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Arabino-Heptulosonate, Synthase, Shikimate, Dahp, Dah7P, Dahps, Dah7Ps, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. R. Schofield, B. F. Anderson, M. L. Patchett, G. E. Norris, G. B. Jameson, E. J. Parker
Substrate Ambiguity And Crystal Structure Of Pyrococcus Furiosus 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase: An Ancestral 3-Deoxyald-2-Ulosonate-Phosphate Synthase?(, )
Biochemistry V. 44 11950 2005
PubMed-ID: 16142893 | Reference-DOI: 10.1021/BI050577Z
(for further references see the PDB file header)

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOHEPTONATE ALDOLASE
	Chains	:	A, B
	EC Number	:	4.1.2.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261
	Synonym	:	DAH7PS, 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MN	1	Ligand/Ion	MANGANESE (II) ION
3	PEP	2	Ligand/Ion	PHOSPHOENOLPYRUVATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	PEP	4	Ligand/Ion	PHOSPHOENOLPYRUVATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:114 , ARG A:115 , PEP A:901	BINDING SITE FOR RESIDUE CL A 902
2	AC2	SOFTWARE	CYS B:31 , HIS B:201 , GLU B:227 , ASP B:238	BINDING SITE FOR RESIDUE MN B 900
3	AC3	SOFTWARE	GLY B:113 , ALA B:114 , ARG B:115 , PEP B:1901	BINDING SITE FOR RESIDUE CL B 1902
4	AC4	SOFTWARE	ARG A:55 , GLN A:111 , GLY A:113 , ALA A:114 , ARG A:115 , LYS A:136 , ARG A:166 , ASP A:198 , HIS A:201 , CL A:902 , HOH A:904	BINDING SITE FOR RESIDUE PEP A 901
5	AC5	SOFTWARE	ARG B:55 , LYS B:60 , GLN B:111 , ALA B:114 , ARG B:115 , LYS B:136 , ARG B:166 , HIS B:201 , CL B:1902 , HOH B:1904	BINDING SITE FOR RESIDUE PEP B 1901

(no "SS Bond" information available for 1ZCO)

(no "Cis Peptide Bond" information available for 1ZCO)

(no "SAP(SNP)/Variant" information available for 1ZCO)

(no "PROSITE Motif" information available for 1ZCO)

(no "Exon" information available for 1ZCO)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:262
 aligned with Q8U0A9_PYRFU | Q8U0A9 from UniProtKB/TrEMBL  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
         Q8U0A9_PYRFU     1 MKYSKEYKEKTVVKINDVKFGEGFTIIAGPCSIESRDQIMKVAEFLAEVGIKVLRGGAFKPRTSPYSFQGYGEKALRWMREAADEYGLVTVTEVMDTRHVELVAKYSDILQIGARNSQNFELLKEVGKVENPVLLKRGMGNTIQELLYSAEYIMAQGNENVILCERGIRTFETATRFTLDISAVPVVKELSHLPIIVDPSHPAGRRSLVIPLAKAAYAIGADGIMVEVHPEPEKALSDSQQQLTFDDFLQLLKELEALGWKG 262
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zcoA00 A:1-262 Aldolase class I                                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eee....eeeee.....hhhhhhhhhhhhhhh...eee................hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhh.....eeee.....hhhhhhhhhhhhhh.....eeeee................hhhhhhhhhh...eee.......hhhhhhhhhhhhhhh...eeeee...hhhhh........hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zco A   1 MKYSKEYDEKTVVKINDVKFGEGFTIIAGPCSIESREQIMKVAEFLAEVGIKVLRGGAFKPRTSPYSFQGYGEKALRWMREAADEYGLVTVTEVMDTRHVELVAKYSDILQIGARNSQNFELLKEVGKVENPVLLKRGMGNTIQELLYSAEYIMAQGNENVILCERGIRTFETATRFTLDISAVPVVKELSHLPIIVDPSHPAGRRSLVIPLAKAAYAIGADGIMVEVHPEPEKALSDSQQQLTFDDFLQLLKELEALGWKG 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with Q8U0A9_PYRFU | Q8U0A9 from UniProtKB/TrEMBL  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
         Q8U0A9_PYRFU     1 MKYSKEYKEKTVVKINDVKFGEGFTIIAGPCSIESRDQIMKVAEFLAEVGIKVLRGGAFKPRTSPYSFQGYGEKALRWMREAADEYGLVTVTEVMDTRHVELVAKYSDILQIGARNSQNFELLKEVGKVENPVLLKRGMGNTIQELLYSAEYIMAQGNENVILCERGIRTFETATRFTLDISAVPVVKELSHLPIIVDPSHPAGRRSLVIPLAKAAYAIGADGIMVEVHPEPEKALSDSQQQLTFDDFLQLLKELEALGWKG 262
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zcoB00 B:1-262 Aldolase class I                                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eee....eeeee.....hhhhhhhhhhhhhhhh..eee................hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh....eeeee................hhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh........hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zco B   1 MKYSKEYDEKTVVKINDVKFGEGFTIIAGPCSIESREQIMKVAEFLAEVGIKVLRGGAFKPRTSPYSFQGYGEKALRWMREAADEYGLVTVTEVMDTRHVELVAKYSDILQIGARNSQNFELLKEVGKVENPVLLKRGMGNTIQELLYSAEYIMAQGNENVILCERGIRTFETATRFTLDISAVPVVKELSHLPIIVDPSHPAGRRSLVIPLAKAAYAIGADGIMVEVHPEPEKALSDSQQQLTFDDFLQLLKELEALGWKG 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 1ZCO)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Pyrococcus furiosus. Organism_taxid: 2261. (2)

1a	1zcoA00	A:1-262
1b	1zcoB00	B:1-262

(no "Pfam Domain" information available for 1ZCO)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8U0A9_PYRFU | Q8U0A9)

molecular function
	GO:0003849	3-deoxy-7-phosphoheptulonate synthase activity	Catalysis of the reaction: D-erythrose 4-phosphate + H(2)O + phosphoenolpyruvate = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate.
	GO:0016832	aldehyde-lyase activity	Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009073	aromatic amino acid family biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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